No, dragging is about as bad as symlinking. If you have many independent modules that you need to bring together as part of the same product, there are ways to do that (Bundle/Task, Shipwright, Dist::Zilla). For some organizational ideas see http://github.com/bestpractical/shipwright, http://github.com/bricoleurs/.

Should I write some sort of Project::Test module that controls the loading and testing of all the rest?

You could but it isn't essential, prove is pretty good.

Should I really be patching all the .t files with use lib qw{ lib/ }?

No. Let prove/Test::Harness manage @INC.

Should I patch prove?

No, subclass App::Prove :)